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Fig. 4 | Epigenetics & Chromatin

Fig. 4

From: Distinct and overlapping roles of STAG1 and STAG2 in cohesin localization and gene expression in embryonic stem cells

Fig. 4

Dual loss of STAG1 and STAG2 reveals redundant functions. a Genome browser tracks for RAD21 ChIP-seq signal in the four conditions: wild-type siGLO, wild-type siStag1, Stag2−/− siGLO, and Stag2−/− siStag1 cells. b Average signal plots and heatmaps of RAD21 signal at a union peak list from the four conditions. c Venn diagram of DEGs from Stag1−/− siGLO, Stag2−/− siGLO, and Stag2−/− siStag1 cells. d Clustered heatmap of log2 fold changes for a combined list of DEGs in wild-type siStag1, Stag2−/− siGLO, and Stag2−/− siStag1 cells all relative to wild-type siGLO. e Violin plots depicting log2-fold changes of all DEGs, and those within Super-enhancer Domains and Polycomb Domains for wild-type siStag1, Stag2−/− siGLO, and Stag2−/− siStag1 cells all relative to wild-type siGLO. Dotted lines indicate the mean. Asterisks indicate significant differences between groups (****p < 0.0001). f Bar graphs with log2 fold change of expression of cell identity genes including those that represent pluripotency (Pou5f1, Sox2, Nanog), ectoderm (Pax6 and Nestin), and endoderm lineages (Gata6 and Sox17) in wild-type siStag1, Stag2−/− siGLO, and Stag2−/− siStag1 cells, all relative to wild-type siGLO. Asterisks indicate significant differences from wild-type siGLO cells (padj < 0.01). g Bar graph with log2 fold change of expression of genes inside and outside of Super-enhancer Domains in wild-type siStag1, Stag2−/− siGLO, or Stag2−/− siStag1 cells, all relative to wild-type siGLO. Asterisks indicate significant differences from wild-type siGLO cells (padj < 0.01). h Western blot analysis following co-immunoprecipitation of CTCF and cohesin in the four conditions. i Proliferation assay with relative cell number represented as a fraction of original plating density for the four conditions. Asterisks indicate significant differences between groups (****p < 0.0001, **p < 0.01, *p < 0.05). Significance at 72 h is between wild-type siStag1 and Stag2−/− siStag1 conditions

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